BIO9905MERG1 – Bioinformatics for Environmental Sequencing (DNA metabarcoding)

Changes in the course due to coronavirus

Spring 2021 the exams of most courses at the MN Faculty will be conducted as digital home exams or oral exams, using the normal grading scale. The semester page for your course will be updated with any changes in the form of examination.

See more information about examination at the MN Faculty spring 2021.

Course content

For mapping and exploring communities of both micro- and macroorganisms, high throughput sequencing of environmental DNA has become a powerful approach. One can either analyze the total DNA content to obtain knowledge about which genes are present (DNA metagenomics) or sequence a selected PCR amplified marker (DNA metabarcoding) to obtain information about the taxonomic composition. We will focus on the latter approach in this course. You will be introduced to important analytical bioinformatics approaches from processing of raw sequence data to establishment of the OTU/sample matrix.

Learning outcome

You will be introduced to high throughput sequencing (methods and concepts) and how the DNA metabarcoding sequence data can be analyzed further. Important themes will be (1) filtering and quality assessment of high throughput sequence data, (2) error correction and/or clustering of high throughput sequence data, and (3) taxonomic annotation of high throughput sequence data. We will also touch upon some further downstream analyses, including network analyses.

Admission to the course

PhD candidates from the University of Oslo should apply for classes and register for examinations through Studentweb.

If a course has limited intake capacity, priority will be given to PhD candidates who follow an individual education plan where this particular course is included. Some national researchers’ schools may have specific rules for ranking applicants for courses with limited intake capacity.

PhD candidates who have been admitted to another higher education institution must apply for a position as a visiting student within a given deadline.

Recommended previous knowledge

Basic knowledge in molecular biology and DNA analyses. Basic knowledge in R and some insight in programming/scripting will be highly advantageous.

Teaching

• The course combines lectures (before lunch) and computer labs after lunch each day.
• This is an intensive course over five days.

Examination

A project report will be compulsory and must be submitted two weeks after the course. The report will be marked as passed/not passed.

Examination support material

All examination support material is allowed.

Grading scale

Grades are awarded on a pass/fail scale. Read more about the grading system.

Special examination arrangements, use of sources, explanations and appeals

See more about examinations at UiO